On Fri, Oct 11, 2013, mmalett.nmt.edu wrote:
>
> PFB1.pdb was created through JSME editor and converted from smiles format,
> and ran through antechamber.
>
> ATOM 1 F 0 2.065 -0.898 1.142 0.00 0.00 F+0
The "problem" is above: the residue name is blank. Antechamber uses that to
construct a MOL2 file, but the MOL2 format doesn't really allow blanks there.
I don't think PDB files with blank residue names are really "legal", but
antechamber should check for that, and insert a placeholder. For now, you
should construct PDB-format files that have something other than blanks in the
residue columns (18-20).
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 11 2013 - 18:00:02 PDT
